Atomistry » Cadmium » PDB 5wgr-6fpc » 6enw
Atomistry »
  Cadmium »
    PDB 5wgr-6fpc »
      6enw »

Cadmium in PDB 6enw: X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin

Protein crystallography data

The structure of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin, PDB code: 6enw was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.43 / 2.60
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.878, 180.878, 180.878, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.6

Other elements in 6enw:

The structure of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin also contains other interesting chemical elements:

Gold (Au) 2 atoms
Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin (pdb code 6enw). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin, PDB code: 6enw:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 6enw

Go back to Cadmium Binding Sites List in 6enw
Cadmium binding site 1 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:27.1
occ:0.40
 OE2 A:GLU11 2.4 24.9 1.0
OE1 A:GLU11 2.5 26.0 1.0
CD A:GLU11 2.8 23.3 1.0
O A:HOH415 3.0 13.1 1.0
OG1 A:THR10 3.9 23.7 1.0
CG A:GLU11 4.4 21.6 1.0
NE2 A:GLN120 4.4 27.4 1.0
OE1 A:GLN120 4.7 29.8 1.0
CB A:SER9 4.7 15.5 1.0
N A:THR10 4.9 17.4 1.0
CD A:GLN120 5.0 27.2 1.0

Cadmium binding site 2 out of 10 in 6enw

Go back to Cadmium Binding Sites List in 6enw
Cadmium binding site 2 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:50.1
occ:0.40
 O A:HOH355 2.1 2.0 0.4
OE2 A:GLU53 2.5 23.4 0.4
O A:HOH393 2.5 5.1 0.4
OE2 A:GLU56 2.7 60.6 1.0
OE2 A:GLU53 2.8 29.7 0.6
OE1 A:GLU53 2.8 24.4 0.4
CD A:GLU53 3.0 23.4 0.4
CD A:GLU53 3.5 28.5 0.6
CD A:GLU56 3.7 49.6 1.0
OE1 A:GLU53 3.9 28.5 0.6
O A:HOH375 3.9 43.8 1.0
OE1 A:GLU56 4.2 50.4 1.0
CG A:GLU53 4.4 23.3 0.4
CG A:GLU53 4.6 27.2 0.6
CB A:GLU53 4.7 25.6 0.6
CG A:GLU56 4.9 41.2 1.0
CB A:GLU53 5.0 23.2 0.4

Cadmium binding site 3 out of 10 in 6enw

Go back to Cadmium Binding Sites List in 6enw
Cadmium binding site 3 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:49.4
occ:0.40
 OE1 A:GLU56 2.4 50.4 1.0
OE1 A:GLU60 2.5 56.5 1.0
O A:HOH344 2.6 5.5 0.4
OE2 A:GLU60 3.1 53.2 1.0
CD A:GLU60 3.2 47.7 1.0
CD A:GLU56 3.6 49.6 1.0
OE1 A:GLU53 3.8 28.5 0.6
OE2 A:GLU56 4.4 60.6 1.0
CG A:GLU57 4.5 40.3 1.0
O A:HOH421 4.6 22.1 1.0
CG A:GLU56 4.6 41.2 1.0
CG A:GLU60 4.6 39.8 1.0
O A:HOH393 4.8 5.1 0.4
CD A:GLU53 4.9 28.5 0.6

Cadmium binding site 4 out of 10 in 6enw

Go back to Cadmium Binding Sites List in 6enw
Cadmium binding site 4 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:20.8
occ:0.50
 OD2 A:ASP80 3.0 13.2 1.0
OD1 A:ASP80 3.5 15.0 1.0
CG A:ASP80 3.7 15.8 1.0
O A:HOH341 4.2 38.0 1.0

Cadmium binding site 5 out of 10 in 6enw

Go back to Cadmium Binding Sites List in 6enw
Cadmium binding site 5 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:34.5
occ:0.40
 O A:HOH304 1.8 10.9 0.4
NE2 A:HIS132 2.6 50.8 1.0
CE1 A:HIS132 3.5 50.1 1.0
CD2 A:HIS132 3.6 45.9 1.0
O A:HOH408 4.3 32.6 1.0
ND1 A:HIS132 4.7 46.6 1.0
CD A:CD209 4.7 41.1 0.3
CG A:HIS132 4.7 42.1 1.0

Cadmium binding site 6 out of 10 in 6enw

Go back to Cadmium Binding Sites List in 6enw
Cadmium binding site 6 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:31.5
occ:0.30
 OE1 A:GLU130 2.2 44.7 1.0
CD A:GLU130 3.0 42.7 1.0
OE2 A:GLU130 3.1 57.0 1.0
CL A:CL211 3.3 2.1 0.4
CG A:GLU130 4.5 36.8 1.0
CD A:CD210 4.9 75.5 0.3

Cadmium binding site 7 out of 10 in 6enw

Go back to Cadmium Binding Sites List in 6enw
Cadmium binding site 7 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:70.3
occ:1.00
 SG A:CYS48 2.4 22.5 1.0
CE1 A:HIS49 3.1 50.9 0.5
CB A:CYS48 3.2 19.8 1.0
ND1 A:HIS49 3.3 46.2 0.5
O A:HOH399 3.4 21.1 1.0
NE2 A:HIS49 3.5 55.0 0.5
ND1 A:HIS49 3.6 46.2 0.5
NH1 A:ARG52 3.7 39.0 1.0
CG A:HIS49 3.7 42.6 0.5
N A:HIS49 3.8 23.3 0.5
N A:HIS49 3.8 23.3 0.5
CD2 A:HIS49 3.9 46.6 0.5
C A:CYS48 3.9 20.7 1.0
CD A:ARG52 4.0 33.1 1.0
CA A:CYS48 4.2 19.6 1.0
O A:GLU45 4.2 17.3 1.0
CE1 A:HIS49 4.3 50.9 0.5
CA A:HIS49 4.3 26.6 0.5
CA A:HIS49 4.3 26.6 0.5
O A:CYS48 4.4 18.5 1.0
CG A:HIS49 4.4 42.6 0.5
CZ A:ARG52 4.6 40.0 1.0
CB A:HIS49 4.6 31.8 0.5
CB A:HIS49 4.6 31.8 0.5
NE A:ARG52 4.8 35.9 1.0
O A:HOH383 4.9 15.6 1.0
CG A:GLU45 4.9 37.0 1.0

Cadmium binding site 8 out of 10 in 6enw

Go back to Cadmium Binding Sites List in 6enw
Cadmium binding site 8 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:51.4
occ:0.30
 O A:HOH403 2.4 45.8 1.0
OE1 A:GLU45 2.7 47.0 1.0
O A:HOH328 3.0 16.4 1.0
O A:HOH409 3.5 32.7 1.0
CD A:GLU45 3.6 46.2 1.0
OE2 A:GLU45 3.9 54.8 1.0
O A:HIS173 4.0 0.8 1.0
ND1 A:HIS173 4.5 0.6 1.0
NH1 A:ARG168 4.6 17.8 1.0
CB A:HIS173 4.7 0.7 1.0
CG A:GLU45 4.8 37.0 1.0
NH2 A:ARG168 4.9 16.9 1.0
CG A:HIS173 4.9 0.8 1.0
C A:HIS173 5.0 0.2 1.0

Cadmium binding site 9 out of 10 in 6enw

Go back to Cadmium Binding Sites List in 6enw
Cadmium binding site 9 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:41.1
occ:0.30
 OD2 A:ASP127 2.4 42.3 1.0
CG A:ASP127 3.1 39.2 1.0
OD1 A:ASP127 3.1 37.2 1.0
OG A:SER131 3.5 41.9 1.0
CB A:SER131 4.3 38.0 1.0
CB A:ASP127 4.6 34.9 1.0
CD A:CD205 4.7 34.5 0.4
O A:ASP127 4.8 26.4 1.0

Cadmium binding site 10 out of 10 in 6enw

Go back to Cadmium Binding Sites List in 6enw
Cadmium binding site 10 out of 10 in the X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of X-Ray Structure of AUOXO4-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:75.5
occ:0.33
 OD1 A:ASP127 3.7 37.2 1.0
OG A:SER131 4.1 41.9 1.0
OE1 A:GLU130 4.4 44.7 1.0
O A:HOH459 4.6 30.3 0.3
CG A:ASP127 4.9 39.2 1.0
CD A:CD206 4.9 31.5 0.3

Reference:

D.M.Monti, G.Ferraro, G.Petruk, L.Maiore, F.Pane, A.Amoresano, M.A.Cinellu, A.Merlino. Ferritin Nanocages Loaded with Gold Ions Induce Oxidative Stress and Apoptosis in Mcf-7 Human Breast Cancer Cells. Dalton Trans V. 46 15354 2017.
ISSN: ESSN 1477-9234
PubMed: 29072740
DOI: 10.1039/C7DT02370G
Page generated: Fri Jul 19 19:12:32 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy